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Author SHA1 Message Date
Matt Olm
031fbd37aa
Instrain profile (#1822) 
* add instrain profile

* module instrain/profile

* add instrain profile

* module instrain/profile

* instrain profile

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/instrain/profile/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/instrain/profile/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/instrain/profile/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* update

* linting

* Apply suggestions from code review

* Update modules/instrain/profile/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-30 18:44:41 +02:00
Simon Pearce
d6102dab6d
NGSCheckMate doesn't generate a pdf for only one sample, made optional output (#1839) 
NGSCheckMate doesn't generate a pdf if only one sample is included, made optional

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-06-30 17:43:34 +01:00
Simon Pearce
a363c12d71
Set randomseed for UMI tools if not otherwise set (#1837) 
Set randomseed if not otherwise set

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
 2022-06-30 16:30:38 +01:00
Jose Espinosa-Carrasco
82fdff4fb4
Add khmer unique-kmers.py module (#1838) 2022-06-30 16:23:30 +01:00
Matthias De Smet
44baf85bcc
snapaligner: improve index detection (#1836) 
* improve index detection

* fix escaping
 2022-06-30 12:19:46 +02:00
Matthias De Smet
253f8c1b0e
snapaligner: fix quotes (#1835) 
Fix quotes
 2022-06-30 11:15:15 +02:00
James A. Fellows Yates
486eebfd29
Update RGI: add database version reporting to module (#1824) 
* Add rgi database version to module as fixed within the container/environment

* Remove check of the version file

* Or rather check for existance of the versions file not contents

* Delete main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
 2022-06-29 16:30:51 -06:00
Mahesh Binzer-Panchal
b67556e29f
Add FastK/Merge (#1828) 
* Add FastK/Merge

* Update modules/fastk/merge/main.nf

* Update modules/fastk/merge/meta.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
 2022-06-29 18:04:36 +02:00
Annick Renevey
80746895e2
Update Arriba to 2.3.0 (#1827) 
* update test files md5sum

* update test files md5sum, again
 2022-06-29 14:39:13 +02:00
Matthias De Smet
e2755cb039
add extra output from snap aligner (#1826) 2022-06-29 12:37:38 +02:00
Zhe Wang
0f1e736212
update kb-python version (#1823) 
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
 2022-06-29 11:19:34 +02:00
Alexander Peltzer
08376da684
Bump MultiQC to v1.13a (dev) (#1814) 
* Bump MultiQC to v1.13a (dev)

* Update main.nf

Predicted new container names ;-)
 2022-06-29 08:40:42 +02:00
nvnieuwk
d596571a03
added an optional vcf index to bcftools/norm (#1821) 
* added an optional vcf index to bcftools/norm

* updated test.yml for failing conda tests
 2022-06-28 16:18:12 +02:00
SusiJo
98ffb09002
Added output files to ASCAT (#1820) 
* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml

* added outputs + prefix to outputs

* added test-yml outputs

* change underscores to dots
 2022-06-28 14:45:57 +02:00
Matthias De Smet
a9521de5ac
bclconvert: Update Dockerfile (#1819) 
* Update Dockerfile

* Output only top level InterOp files

* Update tag
 2022-06-28 11:11:16 +01:00
Adam Talbot
009f7c691c
Add module: gatk4/leftalignandtrimvariants (#1808) 
* Added: gatk4/leftalignandtrimvariants

Additions:
 - GATK4/LeftAlignAndTrimVariants module
 - Use sars-ncov2 test data as this normalises a larger INDEL correctly.

Fixes #1801

* fixup: Added index to output spec

* fixup: Pattern of tbi output corrected to 'tbi'

* gatk4/leftalignandtrimvariants: Added intervals

Changes:
 - gatk4/leftalignandtrimvariants now supports optional interval as BED
 file
 - Tests added with and without interval. Not test BED file excludes all
 variants so no variants are actually normalised.

Fixes #1801

* fixup: leftalignandtrimvariants vcf->tbi fix

* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
 2022-06-28 10:44:08 +02:00
Alexander Peltzer
b573ff053e
Bugfix for CellRanger Dockerfile (#1812) 
Bugfix to enable Singularity support
 2022-06-27 11:07:33 +02:00
Mahesh Binzer-Panchal
233fa70811
Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
Merlin Szymanski
b6fe5d2643
Add Atlas/PMD (#1810) 
* add atlas/pmd
* update atlas/pmd tests
* Add atlas/PMD module
* Remove comment
* Run Prettier
* Incorporate Review by @jfy133

Co-authored-by: maxibor <maxime.borry@gmail.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-24 16:53:51 +02:00
FriederikeHanssen
9b51362a53
Proposal: Rename output from fastp module (#1802) 
* Rename output from fastp module

* UPdate tests

* fix alignment

* prettier

* Update modules/fastp/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>

* apply review suggestion -sf

* typo

* update md5

* update md5

* try with human data

* revert, human data also doesn't work

* use contains instead

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-06-24 10:01:14 +02:00
nvnieuwk
1363130410
small changes to vcfanno (#1804) 
removed a redundant input field from vcfanno

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-06-24 08:58:26 +02:00
Matthias De Smet
5e2325956c
bump bclconvert version (#1806) 2022-06-24 07:14:42 +02:00
Mahesh Binzer-Panchal
a7193dc628
Add MerquryFK KatGC (#1798) 
* Add KAT GC

* Add additional container warning
 2022-06-23 20:57:15 +02:00
Thomas A. Christensen II
2f0b192404
Add KAIJU2KRONA module (#1800) 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-23 16:38:50 +00:00
SusiJo
7daba6a13f
Update ASCAT module (#1805) 
* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml
 2022-06-23 17:06:00 +02:00
Felipe Marques de Almeida
e1a3ae6bf5
make module output meta map (#1803) 2022-06-23 12:43:06 +02:00
James A. Fellows Yates
9d7208504d
Add gecco/run module (#1790) 
* Add gecco/run module

* Fix container URLs

* Apply suggestions from code review

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
 2022-06-22 13:43:45 +02:00
Mahesh Binzer-Panchal
280eec5317
Add MerquryFK KatComp (#1797) 
Add Kat Comp

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-21 09:43:37 +02:00
Adam Talbot
f19ec865aa
vcf2maf module with built in VEP (#1768) 
vcf2maf module created

Additions:
 - vcf2maf module created
 - If VEP is present in PATH, it is added to command
 - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
 - VEP version automatically added to versions.yml
 - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
 - Default Docker image includes VEP and vcf2maf
 - Test includes without VEP.

Relates to #490
 2022-06-20 18:27:12 +02:00
James A. Fellows Yates
be8d7b3293
Update MALT to older version due to major bug in most recent version (#1796) 
* Rollback version

* Start work rollback to 0.4.1

* Further changes

* Re do dynamic flag creation

* Prettier.
 2022-06-20 08:20:22 +02:00
nvnieuwk
6e7c0e945b
new module vcf2db (#1795) 
* added vcf2db

* fix test.yml

* possible fix for failing tests

* fix version number

* fix test.yml

* removed some comments
 2022-06-17 15:54:02 +02:00
alyssa-ab
c1eb9cce44
Trimmomatic (#1757) 
* Trimmomatic main only first draft

* Add test files

* SE PE Adjustment

* Remove extra reads input

* chore: Remove TODOs

* Apply suggestions from code review

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* fix(trimmomatic): Handle SE output correctly

Since there's never going to be unpaired reads for SE reads we can get
away with it for SE

* fix(trimmomatic): Use correct elvis operator to handle logic

* fix(trimmomatic): Add hack to work with SE and PE reads

* Update test.yml

* use the PE and SE trimming correctly

* Made user set adaptors

* Add documentation

* test(trimmomatic): Add files to pytest_modules

* test(trimmomatic): Update name of failing test

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
 2022-06-17 13:18:15 +00:00
Sébastien Guizard
8296a28346
Remove a blank line (#1793) 2022-06-17 10:58:24 +01:00
Maxime U. Garcia
757c20c8eb
Same version on conda and in the dockerfile (#1791) 2022-06-16 16:25:54 +02:00
Matthias De Smet
f32dc15414
update bclconvert module, as used in nf-core/demultiplex (#1569) 
* update bclconvert module, as used in nf-core/demultiplex

* reconfigure test with new test data

* update test

* formatting

* update outputs, update meta

* update module and test

* update test config, test.yml

* fix linting

* emit logs and reports as dir

* fix typo, recreate test.yml

* fix linting

Co-authored-by: CMGG ICT Team <ict@cmgg.be>
 2022-06-16 15:03:13 +02:00
FriederikeHanssen
1ac223ad43
GATK/Getpileupsummaries: If no intervals use variants instead (#1787) 
If no intervals use variants instead
 2022-06-16 15:00:01 +02:00
Matthias De Smet
ecece498f1
samtools/*stats*: use prefix for outputs (#1788) 
* use prefix in flagstat

* use prefix in idxstats

* use prefix in stats

* update test.yml
 2022-06-16 13:42:01 +02:00
Robert A. Petit III
052b9f2fe9
add module for plasmidfinder (#1773) 
* add module for plasmidfinder

* Update test.yml
 2022-06-15 10:25:51 -06:00
Robert A. Petit III
1fe4cb942f
add module for ariba (#1731) 2022-06-15 10:18:31 -06:00
Anders Sune Pedersen
30f72e2482
Optional output from the VEP-moduel (#1775) 
* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774

* Trying to fix tests

* Still trying to fix tests

* Fetching the vep-output-file-extension from the args.

* Update meta.yml

* WIP: Adding tests for vep-output json and tab

* updated the test.yml

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
 2022-06-15 13:52:12 +02:00
nvnieuwk
9dbaffff88
fix bgziptabix extension (#1784) 
* fix bgziptabix extension

* update test.yml
 2022-06-15 10:33:10 +02:00
Mahesh Binzer-Panchal
0af6adef55
Add MerquryFK PloidyPlot (#1780) 2022-06-14 20:50:58 +02:00
Mahesh Binzer-Panchal
e91e99db30
Add GeneScopeFK (#1781) 2022-06-14 20:49:06 +02:00
Mahesh Binzer-Panchal
8ded6d441a
Add MerquryFK (#1778) 
* Add MerquryFK

* Change resource allocation
 2022-06-14 16:36:02 +02:00
Mahesh Binzer-Panchal
fd5aea0b76
Add FastK/Histex (#1776) 2022-06-14 16:30:37 +02:00
nvnieuwk
1a4ab76618
new module rtgtools/pedfilter (#1777) 
* new module rtgtools/pedfilter

* removed checksum due to the presence of a date in the file
 2022-06-14 16:02:18 +02:00
Mahesh Binzer-Panchal
4e308c131e
FastK/fastK (#1739) 
* Add FastK/FastK

* Add ktab and prof outputs

* Add the hidden files necessary for the optional files

* Update image

* Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
 2022-06-14 13:39:52 +02:00
Thomas A. Christensen II
8b2a473f58
New module: krakentools/kreport2krona (#1746) 
* Add module definition for kreport2krona

* Add metadata for kreport2krona module

* Add tests for kreport2krona

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
 2022-06-13 20:14:44 +02:00
Maxime U. Garcia
b689b8ed88
TIDDIT - add --skip_assembly when no bwa specified (#1769) 
add --skip_assembly when no bwa specified
 2022-06-13 17:02:59 +02:00
Maxime U. Garcia
680b6c5b04
Update tiddit to 3.1.0 (#1767) 
* update TIDDIT to 3.1.0

* update VCF too as version is in file
 2022-06-13 16:24:34 +02:00